In the current version, content created with theme sections cannot be included in the table of contents.
RuffRuff Table of Contents generates the TOC by parsing HTML heading tags (H1–H6) found in blog post body text (article.content), product descriptions (product.content), page content (page.content), and collection descriptions (collection.description).
Content added via Shopify sections (page builder blocks) exists in a separate part of the DOM and is not currently supported as a TOC source.